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Comparative Analysis of Mitochondrial Genomes of Geographic Variants Of www.nature.com/scientificreports OPEN Comparative analysis of mitochondrial genomes of geographic variants of the gypsy Received: 8 August 2017 Accepted: 11 October 2017 moth, Lymantria dispar, reveals a Published: xx xx xxxx previously undescribed genotypic entity Abdelmadjid Djoumad1, Audrey Nisole1, Reza Zahiri2, Luca Freschi3, Sandrine Picq 1,3, Dawn E. Gundersen-Rindal4, Michael E. Sparks4, Ken Dewar5, Don Stewart1, Halim Maarouf 3, Roger C. Levesque3, Richard C. Hamelin3,6 & Michel Cusson 1,3 The gypsy moth, Lymantria dispar L., is one of the most destructive forest pests in the world. While the subspecies established in North America is the European gypsy moth (L. dispar dispar), whose females are fightless, the two Asian subspecies, L. dispar asiatica and L. dispar japonica, have fight- capable females, enhancing their invasiveness and warranting precautionary measures to prevent their permanent establishment in North America. Various molecular tools have been developed to help distinguish European from Asian subspecies, several of which are based on the mitochondrial barcode region. In an efort to identify additional informative markers, we undertook the sequencing and analysis of the mitogenomes of 10 geographic variants of L. dispar, including two or more variants of each subspecies, plus the closely related L. umbrosa as outgroup. Several regions of the gypsy moth mitogenomes displayed nucleotide substitutions with potential usefulness for the identifcation of subspecies and/or geographic origins. Interestingly, the mitogenome of one geographic variant displayed signifcant divergence relative to the remaining variants, raising questions about its taxonomic status. Phylogenetic analyses placed this population from northern Iran as basal to the L. dispar clades. The present fndings will help improve diagnostic tests aimed at limiting risks of AGM invasions. Te gypsy moth, Lymantria dispar (Linnaeus, 1758) (Insecta: Lepidoptera: Erebidae: Lymantriinae), is consid- ered one of the most destructive forest defoliators over much of its range. In North America alone, losses and population suppression operations targeting this species are estimated at $3.2 billion each year1. Currently, L. dispar comprises three recognized sub-species2 based on morphological criteria, female fight capability and geo- graphic origins: L. dispar dispar Linnaeus, found over most of western Europe (“EGM” for European Gypsy Moth) and North Africa, and accidentally introduced from France into North America in 18693, L. dispar asiatica Vnukovskij, distributed over much of continental Asia, including Russia, China and the Korean peninsula, and L. 1Laurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, 1055 rue du PEPS, Quebec City, Quebec, G1V 4C7, Canada. 2Canadian Food Inspection Agency, Ottawa Plant Laboratory, Entomology Unit, Ottawa, Ontario, Canada. 3Institute for Integrative and System Biology, 1030 Avenue de la Médecine, Université Laval, Quebec City, Quebec, G1V 0A6, Canada. 4United States Department of Agriculture - ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland, 20705, United States of America. 5McGill University and Genome Quebec Innovation Centre, 740 Dr. Penfeld Avenue Rm 7104, Montreal, Quebec, H3A 0G1, Canada. 6University of British Columbia, Vancouver, British Columbia, Canada. Abdelmadjid Djoumad, Audrey Nisole and Reza Zahiri contributed equally to this work. Correspondence and requests for materials should be addressed to M.C. (email: [email protected]) SCIENTIFIC REPORTS | 7: 14245 | DOI:10.1038/s41598-017-14530-6 1 www.nature.com/scientificreports/ COI Map (Fig. 1) Name Species1 marker Origin Region Supplier 1 Ldd_NJ L. dispar dispar USA New Jersey D. Gundersen-R3 2 Ldd_KG L. dispar dispar Greece Kavála, Macedonia M. Keena4 EGM 3 Ldd_LJ L. dispar dispar Lithuania Juodkrante, Kuzsin Nezijos M. Keena4 4 Ldd_KZ L. dispar dispar Kazakhstan Chuy Valley S.K. Korb5 5 Ldd_RB L. dispar dispar Russia Krasnoyarsk, Siberia M. Keena4 6 Lda_TJ L. dispar asiatica China Tianjin H. Nadel6 7 Lda_RM L. dispar asiatica Russia Primorski, far east M. Keena4 AGM 8 Ldj_JN L. dispar japonica Japan Honshu M. Keena4 9 Ldj_ID L. dispar japonica Japan Iwate district H. Nadel6 10 Lu_JH L. umbrosa umbrosa Japan Hokkaido C. Hideyuki7 11 L?_IR2 L. dispar? dispar? Iran Noor, Mazandaran H. Rajaei8 Table 1. List of the Lymantria specimens processed for mitogenome sequencing. 1As determined using TaqMan assay8. 2Initially considered to be L. dispar dispar on the basis of TaqMan assay results8; results of full mitogenome analysis subsequently called this conclusion into question. 3USDA, Beltsville, Maryland, USA. 4US Forest Service, Hamden, CT, USA. 5Russian Entomological Society, Nizhny Novgorod, Russia. 6USDA APHIS, Buzzards Bay, MA, USA. 7Bernice Pauahi Bishop Museum, Honolulu, USA. 8State Museum of Natural History, Stuttgart, Germany. dispar japonica Motschulsky, which appears to be confned to Japan (Honshu, Shikoku, Kyushu and Hokkaido). For regulatory purposes, the latter two subspecies, along with three other closely related Japanese Lymantria spe- cies (i.e., L. umbrosa Butler, L. postalba Inoue and L. albescens Hori and Umeno), are generally considered “Asian gypsy moth” (AGM)2. Unlike their European counterpart, the two Asian L. dispar subspecies have fight-capable females4,5 and a broader host range6, considerably increasing the risks of rapid propagation relative to EGM. With the current intensifcation of commercial trade with Asia, AGM introduction and establishment into North America are considered a very signifcant threat. AGM specimens are regularly intercepted at North American ports, and accidental introductions have occurred, resulting in costly eradication campaigns7. Te rigorous and rapid identifcation of intercepted gypsy moth samples suspected of being AGM and an assessment of their geographic origins are critical to the negotiations undertaken by North American regula- tory agencies with their Asian trading partners in an efort to reduce risks of accidental introductions. However, morphological characters provide little useful information for species and subspecies delineation and for the identifcation of source countries, particularly when dealing with the immatures stages (e.g., eggs and larvae). As a consequence, many studies have examined the usefulness of molecular markers to help distinguish gypsy moth subspecies and to identify the geographic origins of intercepted specimens (see8). In this respect, a 658 bp fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene has received much attention, given its recognized efectiveness in delineating taxa9. However, although the COI 5’ barcode region could easily separate the European from the two Asian subspecies, it proved inadequate to distinguish L. d. asiatica from L. d. japon- ica8,10,11. On the other hand, distinct regions of the mitochondrial genome, including the 3′ portion of the COI gene8 and fve other genes12 (ND2, ND6, ATP6, ATP8 and CytB) provided resolution of the two Asian strains, pointing to the informativeness of alternative mitochondrial regions. With respect to identifying the geographic origins of gypsy moth specimens, previous work has shown that the COI barcode alone could provide some clues as to the source of unknown samples10,11, and that other mitochon- drial genes could also be useful for this purpose12. While analysis of nuclear markers such as microsatellites12 and genome-wide SNPs13 points to their remarkable value in identifying the geographic origins of gypsy moth spec- imens, mitochondrial genomes should not be underestimated as a potential source of markers to help identify geographic variants, especially in view of their high substitution rate relative to nuclear genomes14,15. For the present study, we undertook the sequencing of the entire mitochondrial genome of 10 geographic variants of Lymantria dispar, with a good coverage of this species’ geographic range and inclusion of two or more variants of each subspecies; the closely related L. umbrosa was selected as outgroup. Only three L. dispar mito- chondrial genomes had previously been sequenced and deposited in GenBank, each with limited information about the origin and subspecies designation of the insect from which they were obtained (accession numbers: FJ617240, GU994783, GU994784). Here, we present a detailed comparative analysis of gypsy moth mitochondrial genomes with the aim of assessing their usefulness for subspecies delimitation and identifcation of geographic origins. Interestingly, the mitochondrial genome of one of the geographic variants sampled in this study displayed important diferences relative to the remaining variants. We thus conducted phylogenetic analyses to help shed light on the potential taxonomic position of this previously uncharacterized geographic variant. Results Lymantria dispar mitochondrial genome organization. A total of 11 mitochondrial genomes of Lymantria specimens (Table 1; Fig. 1) were completely sequenced, assembled and annotated (Table 2). While one of these specimens was L. umbrosa, the other 10 specimens were originally considered to be geographic variants of L. dispar. However, one sample from northern Iran (referred to here as L?_IR) displayed important diferences relative to the other L. dispar mitogenomes, calling into question its taxonomic status (see details in the next SCIENTIFIC REPORTS | 7: 14245 | DOI:10.1038/s41598-017-14530-6 2 www.nature.com/scientificreports/ Figure
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